tokenization_molformer.py

# coding=utf-8
# Copyright 2023 The HuggingFace Inc. team. All rights reserved.
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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
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"""Tokenization classes for Molformer."""

import collections
import json
import os
import re
from typing import List, Optional, Tuple

from transformers.tokenization_utils import PreTrainedTokenizer
from transformers.utils import logging


logger = logging.get_logger(__name__)

VOCAB_FILES_NAMES = {"vocab_file": "vocab.json"}

PRETRAINED_VOCAB_FILES_MAP = {
    "vocab_file": {
        "ibm/MoLFormer-XL-both-10pct": "https://huggingface.co/ibm/MoLFormer-XL-both-10pct/resolve/main/vocab.json",
    }
}

PRETRAINED_POSITIONAL_EMBEDDINGS_SIZES = {
    "ibm/MoLFormer-XL-both-10pct": 202,
}


class MolformerTokenizer(PreTrainedTokenizer):
    r"""
    Construct a Molformer tokenizer. Based on regex.

    This tokenizer inherits from [`PreTrainedTokenizer`] which contains most of the main methods. Users should refer to
    this superclass for more information regarding those methods.

    Args:
        vocab_file (`str`):
            File containing the vocabulary.
        unk_token (`str`, *optional*, defaults to `"<unk>"`):
            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
            token instead.
        sep_token (`str`, *optional*, defaults to `"<eos>"`):
            The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for
            sequence classification or for a text and a question for question answering. It is also used as the last
            token of a sequence built with special tokens.
        pad_token (`str`, *optional*, defaults to `"<pad>"`):
            The token used for padding, for example when batching sequences of different lengths.
        cls_token (`str`, *optional*, defaults to `"<bos>"`):
            The classifier token which is used when doing sequence classification (classification of the whole sequence
            instead of per-token classification). It is the first token of the sequence when built with special tokens.
        mask_token (`str`, *optional*, defaults to `"<mask>"`):
            The token used for masking values. This is the token used when training this model with masked language
            modeling. This is the token which the model will try to predict.
    """

    vocab_files_names = VOCAB_FILES_NAMES
    pretrained_vocab_files_map = PRETRAINED_VOCAB_FILES_MAP
    max_model_input_sizes = PRETRAINED_POSITIONAL_EMBEDDINGS_SIZES
    model_input_names = ["input_ids", "attention_mask"]

    def __init__(
        self,
        vocab_file,
        unk_token="<unk>",
        sep_token="<eos>",
        pad_token="<pad>",
        cls_token="<bos>",
        mask_token="<mask>",
        **kwargs,
    ):
        if not os.path.isfile(vocab_file):
            raise ValueError(
                f"Can't find a vocabulary file at path '{vocab_file}'. To load the vocabulary from an IBM pretrained"
                " model use `tokenizer = AutoTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)`"
            )
        with open(vocab_file, encoding="utf-8") as vocab_handle:
            self.vocab = json.load(vocab_handle)
        self.ids_to_tokens = collections.OrderedDict([(ids, tok) for tok, ids in self.vocab.items()])
        self.pattern = (
            r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>|\*|\$|\%[0-9]{2}|[0-9])"
        )
        self.regex_tokenizer = re.compile(self.pattern)

        super().__init__(
            unk_token=unk_token,
            sep_token=sep_token,
            pad_token=pad_token,
            cls_token=cls_token,
            mask_token=mask_token,
            **kwargs,
        )

    @property
    def vocab_size(self):
        return len(self.vocab)

    def get_vocab(self):
        return dict(self.vocab, **self.added_tokens_encoder)

    def _tokenize(self, text):
        split_tokens = self.regex_tokenizer.findall(text)
        return split_tokens

    def _convert_token_to_id(self, token):
        """Converts a token (str) in an id using the vocab."""
        return self.vocab.get(token, self.vocab.get(self.unk_token))

    def _convert_id_to_token(self, index):
        """Converts an index (integer) in a token (str) using the vocab."""
        return self.ids_to_tokens.get(index, self.unk_token)

    def convert_tokens_to_string(self, tokens):
        """Converts a sequence of tokens (string) in a single string."""
        out_string = "".join(tokens).strip()
        return out_string

    # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.build_inputs_with_special_tokens
    def build_inputs_with_special_tokens(
        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
    ) -> List[int]:
        """
        Build model inputs from a sequence or a pair of sequence for sequence classification tasks by concatenating and
        adding special tokens. A BERT sequence has the following format:

        - single sequence: `[CLS] X [SEP]`
        - pair of sequences: `[CLS] A [SEP] B [SEP]`

        Args:
            token_ids_0 (`List[int]`):
                List of IDs to which the special tokens will be added.
            token_ids_1 (`List[int]`, *optional*):
                Optional second list of IDs for sequence pairs.

        Returns:
            `List[int]`: List of [input IDs](../glossary#input-ids) with the appropriate special tokens.
        """
        if token_ids_1 is None:
            return [self.cls_token_id] + token_ids_0 + [self.sep_token_id]
        cls = [self.cls_token_id]
        sep = [self.sep_token_id]
        return cls + token_ids_0 + sep + token_ids_1 + sep

    # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.get_special_tokens_mask
    def get_special_tokens_mask(
        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None, already_has_special_tokens: bool = False
    ) -> List[int]:
        """
        Retrieve sequence ids from a token list that has no special tokens added. This method is called when adding
        special tokens using the tokenizer `prepare_for_model` method.

        Args:
            token_ids_0 (`List[int]`):
                List of IDs.
            token_ids_1 (`List[int]`, *optional*):
                Optional second list of IDs for sequence pairs.
            already_has_special_tokens (`bool`, *optional*, defaults to `False`):
                Whether or not the token list is already formatted with special tokens for the model.

        Returns:
            `List[int]`: A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token.
        """

        if already_has_special_tokens:
            return super().get_special_tokens_mask(
                token_ids_0=token_ids_0, token_ids_1=token_ids_1, already_has_special_tokens=True
            )

        if token_ids_1 is not None:
            return [1] + ([0] * len(token_ids_0)) + [1] + ([0] * len(token_ids_1)) + [1]
        return [1] + ([0] * len(token_ids_0)) + [1]

    # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.create_token_type_ids_from_sequences
    def create_token_type_ids_from_sequences(
        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
    ) -> List[int]:
        """
        Create a mask from the two sequences passed to be used in a sequence-pair classification task. A BERT sequence
        pair mask has the following format:

        ```
        0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1
        | first sequence    | second sequence |
        ```

        If `token_ids_1` is `None`, this method only returns the first portion of the mask (0s).

        Args:
            token_ids_0 (`List[int]`):
                List of IDs.
            token_ids_1 (`List[int]`, *optional*):
                Optional second list of IDs for sequence pairs.

        Returns:
            `List[int]`: List of [token type IDs](../glossary#token-type-ids) according to the given sequence(s).
        """
        sep = [self.sep_token_id]
        cls = [self.cls_token_id]
        if token_ids_1 is None:
            return len(cls + token_ids_0 + sep) * [0]
        return len(cls + token_ids_0 + sep) * [0] + len(token_ids_1 + sep) * [1]

    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
        if not os.path.isdir(save_directory):
            logger.error(f"Vocabulary path ({save_directory}) should be a directory")
            return
        vocab_file = os.path.join(
            save_directory, (filename_prefix + "-" if filename_prefix else "") + VOCAB_FILES_NAMES["vocab_file"]
        )

        with open(vocab_file, "w", encoding="utf-8") as f:
            f.write(json.dumps(self.vocab, indent=2, sort_keys=True, ensure_ascii=False) + "\n")

        return (vocab_file,)